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Research: Aberrant PRDM9 expression impacts the pan-cancer genomic landscape
- Armande Ang Houle,
- Heather Gibling,
- Fabien C. Lamaze,
- Hilary A. Edgington,
- David Soave,
- Marie-Julie Fave,
- Mawusse Agbessi,
- Vanessa Bruat,
- Lincoln D. Stein,
- and Philip Awadalla
Genome Res. November 2018 28: 1611-1620; Published in Advance October 19, 2018, doi:10.1101/gr.231696.117
...encyclopedia of DNA elements in the human . Nature 489: 57–74. ↵Eram MS, Bustos SP, Lima-Fernandes E, Siarheyeva A, Senisterra G, Hajian T, Chau I, Duan S, Wu H, Dombrovski L, et al. 2014. Trimethylation of histone H3 lysine 36 by human methyltransferase PRDM9 protein. J Biol Chem 289: 12177...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
...of the experimental data sets.For each hotspot, we also inferred the fraction of reads that originated from the B6 and the CAST chromosomes respectively, as previously described (Davies et al. 2016). PRDM9 has a histone methyltransferase activity, and binding to its target sites is associated with trimethylation of H...
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Research: In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
- Corinne Grey,
- Julie A.J. Clément,
- Jérôme Buard,
- Benjamin Leblanc,
- Ivo Gut,
- Marta Gut,
- Laurent Duret,
- and Bernard de Massy
Genome Res. April 2017 27: 580-590; Published in Advance March 23, 2017, doi:10.1101/gr.217240.116
.... cerevisiae, these hotspots are not preferentially located in promoter regions, but they are enriched in H3K4me3 (Buard et al. 2009; Smagulova et al. 2011), presumably through PRDM9 methyltransferase activity (Hayashi et al. 2005). Indeed, PRDM9 can methylate histone H3 at K4, K9, and K36 in vitro (Wu et al...
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Research: PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration
- Christopher L. Baker,
- Michael Walker,
- Shimpei Kajita,
- Petko M. Petkov,
- and Kenneth Paigen
Genome Res. May 2014 24: 724-732; Published in Advance March 6, 2014, doi:10.1101/gr.170167.113
.... Their locations are predominantly determined by the zinc finger protein PRDM9, which binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3). This sets the stage for double-strand break (DSB) formation and reciprocal exchange of DNA between chromatids...
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Research: Rare allelic forms of PRDM9 associated with childhood leukemogenesis
- Julie Hussin,
- Daniel Sinnett,
- Ferran Casals,
- Youssef Idaghdour,
- Vanessa Bruat,
- Virginie Saillour,
- Jasmine Healy,
- Jean-Christophe Grenier,
- Thibault de Malliard,
- Stephan Busche,
- Jean-François Spinella,
- Mathieu Larivière,
- Greg Gibson,
- Anna Andersson,
- Linda Holmfeldt,
- Jing Ma,
- Lei Wei,
- Jinghui Zhang,
- Gregor Andelfinger,
- James R. Downing,
- Charles G. Mullighan,
- and Philip Awadalla
Genome Res. March 2013 23: 419-430; Published in Advance December 5, 2012, doi:10.1101/gr.144188.112
...PRDM9 allelic forms of involvement in the development of preleukemic clones in B-ALL patients andwe propose that PRDM9histoneH3K4 methyltransferase activity in the parental germline could lead to the genomic instability associated with childhood ALL, a plausible mechanismconsistent with the current...
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Research: Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome
- Erik Axelsson,
- Matthew T. Webster,
- Abhirami Ratnakumar,
- The LUPA Consortium,
- Chris P. Ponting,
- and Kerstin Lindblad-Toh
Genome Res. January 2012 22: 51-63; Published in Advance October 17, 2011, doi:10.1101/gr.124123.111
...and inactive in dogs. Axelsson et al. 58 Genome Research www..org Recombination initiation in dogs The PRDM9 protein contains a SET methyltransferase domain, which induces a histonemodification in the vicinity of a sequence motif bound by a zinc finger domain. This modification serves as a mark...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...events are mainly restricted to regions that contain specific motifs that act as binding sites for the PR/SET domain 9 (PRDM9) protein that marks regions for double-stranded breaks, which are repaired by recombination during meiosis (Baudat et al. 2010; Myers et al. 2010; Parvanov et al. 2010). Species...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...-mediated repression allows activation of ERV enhancers upon entry into meiosis. This regulatory feature is observed for independently evolved KZFPs and ERVs in mice and humans, suggesting evolutionary conservation in mammals. Further, we show that KZFP-targeted ERVs are underrepresented on the sex chromosomes...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
..., calculated for ES cell and meiotic data sets. Elevated RNAPII occupancy during meiosis appears to be associated with increased DSB formation (black arrow). (E) Overlap of ChromHMM histone annotations with PRDM9 sites. Note DSB-favored sites are depleted for unmarked chromatin while enriched for H3K36me3...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...histone H3K4me3 and H3K36me3 (Mihola et al. 2009; Baudat et al. 2010; Myers et al. 2010; Parvanov et al. 2010; Grey et al. 2011, 2017; Brick et al. 2012; Lange et al. 2016; Powers et al. 2016). As a consequence, PRDM9-dependent SPO11 hotspots occur in nucleosome-depleted regions with well...

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